Transformations
by tobias foxdemon
Summary: Something strange is going on at the new Team Rocket hideout. When Mewtwo and Mew are sent to investigate, they will soon face a terrible danger beyond imagination. Please review!
1. The Meeting

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_If you review, then I might be motivated to finish it..._

**Transformations**

**Part I**

**Chapter 1**

**The Meeting**

Darkness was all that the pokemon could see beyond the steel bars of its cage. It lay motionless on the cold floor of its enclosure. The small, furry creature picked up its head as it heard lumbering footsteps draw near its cage. Suddenly a gloved hand forced its way into the cage and picked up the squirming pokemon hastily. The pokemon fought back pitifully, but it was no use. The gloved hand quickly shoved the creature into a bag and knotted the top. The animal struggled inside the bag as the human walked. All the pokemon's attempts to escape were futile. All it could do was wait.

Mewtwo carefully examined the rock he was holding, and then threw it into the dark, motionless river that winded slowly through the cave. After staring at the ripples on the surface of the river, he slowly walked over to a large, flat rock that served as his chair and sat down. He drummed his paw against the hard surface of the rock.

Tap tap

Tap

Tap tap

Tap

…

…

Mewtwo heard loud whooshing noises that sounded a lot like wings flapping. Zubats aren't that large, and neither are golbats. I wonder what could be making that noise…

Suddenly, out of nowhere, a massive dragonite burst onto the scene, nearly causing Mewtwo to fall flat on his face.

"Gaaah!! You scared me! What are you doing here? I haven't seen you in months! What brings you here to the Unknown dungeon?"

The dragonite brushed off its scales and stood up quickly.

"You are invited to attend a meeting held by the legendary pokemon. They did not tell me the details of the meeting, but they strongly urge you to come. They mentioned that 'You would be actually be interested about this one."

Mewtwo rolled his eyes, remembering how boring the last meeting was. Topics such as "How to avoid trainers in the wild" didn't exactly strike his fancy, especially when hardly anyone came into the Unknown dungeon anyway. That wasn't the first time he had heard, "You would be actually be interested about this one." Nevertheless, Dragonite's worried eyes convinced him otherwise.

"Fine then. Let everyone know I'm coming."

The creature sat quivering in a new cage. The only difference with this one is that it could actually see outside. Humans in white lab coats with the letter "R" printed on the pocket scurried around outside the cage and computer screens flashed on and off. The pokemon watched as one computer screen showed a animated picture of a rattata slowly turning into a –

All of a sudden, another gloved hand shoved its way into the cage and grabbed the pokemon before it had the chance to even cry out. The animal dropped down into a clear box with a strange, twisted-looking mechanical arm hanging down from the top.

A man strolled over to the box. He was tall, with a short, black haircut and a crisp suit. His presence frightened the pokemon, and it cowered in the corner of the box.

"Now, now Rattata. There's no need to be worried," The man said with a sly grin and an evil gleam in his eyes. " You'll be just fine…"

The mechanical arm suddenly revved to life, and it swung toward the pokemon. A bright red light on the arm's tip suddenly flickered on. The rattata stayed frozen, staring at the light. The red light slowly grew brighter and brighter, and the rattata writhed in agony as red waves of energy rolled through its small body.

Hidden in the wilds somewhere in Kanto, a large group of legendary pokemon gathered in a clearing. Mewtwo paced back and forth, as more pokemon joined the group- including a trio of large birds and a trio of massive cat-like pokemon. Several minutes passed, and then the pokemon formed a large circle. Moments later, an impressive-looking, rainbow colored bird stepped into the center of the circle. Ho-oh cleared its throat and began to speak.

"Fellow legendary pokemon, I have organized this meeting to inform you of one thing: I have reason to believe that Team Rocket has returned!"

The gathering erupted into chaos, as everyone tried to speak at once.

"Silence!!" Ho-oh bellowed.

The commotion ceased.

"I was flying high above the border between Kanto and Johto last week, and I noticed some shady-looking humans walking in and out of Silver cave. I watched them for several more days and I saw machinery being moved inside the cave. All of this seems too suspicious, and I believe Team Rocket is behind it. Why Team Rocket? Because I saw an "R" printed very clearly on the front of everyone's clothing. If the Rockets are behind this disturbance, something terrible is going on, and we need to investigate."

Ho-oh turned toward Mewtwo. " I realize that you have had bad circumstances with them in the past, but I need you to go to the hideout and see what's going on. I believe you have a greater knowledge of Team Rocket than anyone else does at this meeting. You can bring Mew along if you like."

Mew popped out behind Mewtwo and hovered alongside Mewtwo.

Mewtwo closed his eyes and sighed. He remembered his time with Giovanni and the Rockets all to well. Memories flashed before his eyes. Sleep. Dreaming of the ocean, and Mew. Waking up in a giant test tube. Discovering his powers by breaking the glass wall around him with a single thought. Sitting on shards of broken glass, covered in fluids, viewed by the prying eyes of the scientists. Destroying the lab, and flames all around. A helicopter with its blades cutting through the air. Giovanni's offer of unlimited power, ruling the world together as equals. And that promise, broken. If something bad was going on, he had to go.

"I accept."


	2. The Discovery

**Chapter 2**

**The Discovery**

Mewtwo and Mew hovered in the air, concealed by the darkness of night. The frigid air chilled the duo, and their breath was visible in the night air. They watched the cave opening as humans walked in and out.

"So, Mew. Have any bright ideas?"

"Perhaps we should go inside, instead of waiting for something to happen."

"Oh. Brilliant idea. Just, brilliant." Mewtwo shot an icy look at the pink pokemon lingering next to him.

"It's the only way we can find out what's going on. I know that last time the Rockets we around, they tried to capture you. You told the story of that magical lake that cured your wounds and the humans that helped you. I know that you hate the Rockets and you would do anything to exact your revenge against Giovanni."

"It's been years since I last saw him. Maybe I was wrong to assume he was gone for good. I was so careless!"

Mewtwo squeezed his eyes shut and rubbed his forehead with his three-fingered paw.

" Let me guess…he wants to take over the world again! As usual, he can't be creative. Capture this, torture that, destroy this, blah blah blah… I should have never come to the meeting."

Mewtwo turned to Mew. "What do you think? You were never forced to do anything by Giovanni. You haven't even met Giovanni! All I remember is you throwing your pink energy bubbles around and laughing constantly. Annoyed the hell out of me."

"You coward! You can't even admit that you're terrified of the thought of meeting Giovanni again, so you blame everyone around you. You were the one that created that castle on that island in the middle of the ocean. You were the one that created the storm to test those trainers, those innocent victims. You acted very much the same way as Giovanni did. You hid your terror behind that evil mask."

"But now I realize that it was wrong! We almost killed that young boy!"

"No. You did. I was defending him. Defending him from your childish outbursts."

With a wild look in his eyes, Mewtwo pounced on Mew and wrestled her to the ground.

"Aagghh!" he cried.

The tall, feline-like pokemon stopped and stood up. He backed away slowly and sat down again. His head hung in shame.

"I'm sorry Mew. I know that I learned my lesson long ago, but I… sigh. I don't want to return. I'll admit that. But I have no choice. If any other pokemon is going through what I went through… I can't live with that. Let's go inside."

"If you could have controlled your emotions, we could have gone inside fifteen minutes ago." Mew replied with a teasing smile.

"Fine! Just shut up already!"

Mew giggled as the pair made their way inside the cavern.

_------------------------------------------_

Hidden among the rafters of the underground complex, the cloned pair marveled at the sight. Silver cave was alive with activity. Humans went about their business like bees in a hive, constantly moving through the winding rows of desks and lab tables. One human seemed to be conducting an experiment, mixing a blue test tube with a red one. The mixture in the beaker turned purple and started to smoke.

Mewtwo turned his attention towards a large set of swinging double doors in the corner of the cave. The front of the doors read "Level 4 clearance only". He noticed that there was a constant stream of Rockets moving through the doors.

"Mew," The genetic pokemon whispered.

Mew turned her head toward Mewtwo.

"Look at those doors over there. All the higher ranking officials seem to be going there. Something important must be going on in that room."

"You're right! Look at that man. He makes me nervous."

The man in a dark suit strolled toward the double doors. Scientists in while lab coats trailed along beside him. They seemed to be excited, but their eyes revealed something else. Dread. Anxiety.

"Mew. That man is Giovanni. He must on his way to personally survey whatever is behind those doors. We have to make our way in somehow."

"How do you plan to do that? We don't exactly blend in."

Mewtwo scanned the area for any clue of how they could get in. Suddenly his eyes brightened.

"Wait here Mew. I'm going to go in, but I want you to get out of this cave and get away. If there is any sign of trouble, I don't want you to get involved. Get away as fast as you can. I can handle this by myself."

"But…"

"I don't want Giovanni to find out about your existence if I'm captured. You're supposed to be a fossil, remember? This is too risky."

Mewtwo glided over toward the wall on the far side of the cave. Since the cave had so many people in it, he had to be extra careful. He inched his way slowly toward the other side of the cave. After some time, he eyed the double doors, which were now directly below him.

_At least I can't be seen. It's still kind of dark up here. Otherwise I'd be toast._

He raised one paw up and sent an invisible shockwave toward a container marked "Danger: Flammable" on the far side of the room.

_I hope Mew still isn't over there. Probably not. _

The container exploded, sending a huge fireball that extended toward the ceiling. The Rocket workers scrambled to get away from the blaze. There was a mad rush toward the doors as people headed through the emergency exits. Water rained from the ceiling as the sprinkler system turned on.

_Damn, that was foolish. _

Several scientists emerged from the double doors and headed toward the exit. Giovanni followed, flanked by several more Rockets in dark uniforms.

_Well, is the room empty? Did my distraction work?_

Mewtwo waited until all the Rocket's attention was toward the blaze. Then with a single swift movement, he slipped his way through the double doors.


	3. The Capture

**Chapter 3**

**The Capture**

Mew watched as Mewtwo drifted slowly toward the other end of the room. After a while, Mew made her way toward the ceiling and hovered there.

_Mewtwo told me to leave, but I think that I can find some valuable information f I look quickly enough. I wonder what's on those computer screens down there?_

She hesitated for a moment, then dared to take a closer look. No one was around, so she decided to move closer. Mew snuck a look over her shoulder and made sure the coast was clear and hovered right in front of the screen. The screensaver was on, so she wiggled the mouse a little to view what was on the screen. An animation was playing over and over again on the screen.

"Oh my god…" Mew gasped.

Thenwithout warning, everything around Mew turned to flames. The small pink pokemon shielded her eyes as the computer exploded into shards of melted plastic and computer chips. The force of the explosion hurtled her onto the rocky ground.

_Should have… left… like Mewtwo… told me… to… do…_

As the world swirled and started to fade, in her last moments of consciousness, a large silhouette loomed over Mew's battered body, closer… and closer.

_------------------------------------------_

Mewtwo gaped at the sight inside the room, as he saw three humans held in separate cages inside the room. A buff, muscular man with a bald head, a woman with red hair sporting blond streaks, and a small boy with violet hair. They were shabbily dressed in gray one-piece uniforms with Rocket insignias printed on the front. The cages were dark and cold, with a bowl of something, food maybe, in each.

Mewtwo looked around once more in disbelief, then moved closer to the cages.

_Why is Team Rocket holding humans captive? Their own kind! Why? What's going on?_

"Who are you?" Mewtwo asked.

The man looked up at Mewtwo and grunted.

"Why are you here?"

The boy scurried over to the corner of his cage and started to whimper, while the woman stood up and watched cautiously. Mewtwo walked over to the cage closest to him, the woman's.

"What's going on? I need you to tell me."

The woman tossed her hair and continued to stare at Mewtwo.

"You can't talk?"

Mewtwo held up his hands. "I'm not going to hurt you. I'll save you from this prison. Can you understand me?"

The woman started to pace her cell, tossing her head and snorting.

_These people are acting like, animals… Wait… I hear something._

Mewtwo turned around quickly, and became face-to-face with Giovanni.

"Well, well Mewtwo. We meet again. I'm actually impressed by your little diversion; the destruction you caused will take us months to repair. I knew that someone would investigate at one point or another. I came back in once I knew that the fire was contained. But, what a surprise! Mewtwo! I haven't seen you in a while. I see you've met my test subjects. I find them rather, fascinating. Watching their behavior. Listening to their pathetic attempts to speak our language. It's too bad that you came so early, their human intelligence hasn't been integrated into their brain yet…"

"Giovanni!"

"I hear that you have taken refuge in the Unknown Dungeon. How does it feel, being so, alone?"

"Why do you care, you asshole?"

"Oh my! Watch your mouth, Mewtwo." A sly grin tugged on the corners of his mouth. "I realize that you are one of the most powerful pokemon in the world. I know. The last time we met is proof enough. But, I want something from you. More than just your prowess in battle. I want to harness that very power for my own use. Guards!"

Two Rocket grunts entered the room. One of the guards held up a pokeball and presented it to the Rocket leader. Giovanni took the pokeball and started to twiddle it between his thumb and forefinger. He held it up at eye level.

Giovanni held out his other hand, and the Rocket placed a gun into his open palm. Giovanni held the gun against the pokeball.

"I want you to come with me, or the pokemon inside will cease to exist. I believe you would want to see this pokemon again… or I could just…"

"No. Wait."

"Didn't think so. Then you wouldn't see your little pink friend ever again…"

"No!" Mewtwo lunged at Giovanni.

The Rocket leader cocked the gun and laid his finger on the trigger. Mewtwo halted.

"What are you planning now? What have you done with Mew?"

"Nothing, yet. Come with me. Now."

Mewtwo, having no choice, followed Giovanni and the Rocket guards down the corridor leading to another room. The first thing he noticed was series of clear boxes in different sizes lining the edges of the room. Twinkling lights and whirring noises came from the various machines in the room. Several scientists were monitoring the machines. Giovanni nodded at one of them, and the Rocket in a white lab coat came over.

"Get the machine ready."

The man nodded and walked over to a control pad and pressed a button. A door on the side of a medium-sized box opened.

"Put it in."

Mewtwo watched in horror as a scientist dropped the pokeball into the box. The pokeball opened, and Mew emerged.

_Oh no! No! This can't be happening! Mew!_

"I have learned from our last encounter, and I believe that this box is sturdy enough to withstand any attack. All psychic powers should be disabled inside. Now Mewtwo, don't worry. Mew will be just fine…"

Giovanni pointed the gun at Mewtwo as the scientists pressed more controls on the panel. A mechanical arm swung toward the small, pink pokemon lying in the box. A red light shone on Mew's unconscious body. Then the machine started whirring and the light grew stronger with every passing moment.

Giovanni spoke. "Now."

Mewtwo's body stiffened.

Waves of red energy shot out from the arm, enveloping Mew's body. She started to twist and turn in pain, her mouth open in a silent scream.

Mewtwo wanted to help, but somehow he was transfixed and couldn't move. Mew lay, helpless before him, and he couldn't even do anything. Suddenly Mew stopped moving.

"Noooooooooooooo! You've killed her-"

Mewtwo grew quiet as his gaze moved toward his companion again. Somehow, she was… changing. Her arms and legs stretched, and her tail shriveled. Her fur disappeared, leaving pale skin behind. Pink hair grew from her skull.

_My god. My GOD! What has he done!_

Mewtwo collapsed to the floor and crawled over to the box that held Mew. He placed his paws against the smooth, transparent surface. His eyes brimmed with tears as he gazed at the naked human child that lay curled in the center.

_To be continued…_


	4. The Proposal

**Part II**

**Chapter 4**

**The Proposal**

Ho-oh paced nervously on its perch in the Tin tower. Stray feathers littered the floor. It had been more than a day since it had sent Mewtwo and Mew to investigate the Rocket hideout, and Ho-oh was starting to regret sending them.

_I hope they're all right. It's been too long without hearing from them. I have to send a search party. Maybe they need help. I can't live with that possibility._

Ho-oh jumped off its perch, and took off. Soaring through the sky, Ho-oh headed toward Kanto, to the hidden meeting place in the wilds.

_------------------------------------------_

Battered and broken, Mewtwo lay dazed in the middle of another clear box. He tried to take a deep breath, but instead managed to cough up more blood.

_Why… why do they do this? What purpose is there, in torturing me like this…_

He put his paws under his body and shifted to a sitting position.

_If only I could escape._

Mewtwo turned his head toward Mew's cell. She was still unconscious, but now dressed in the gray uniform. The other three humans paced their transparent cells.

For what seemed like the hundredth time, Mewtwo focused his psychic power. He raised one hand and tried to break the locking mechanism with his thoughts. Nothing happened.

_Useless…_

Mewtwo quickly put his hand down as he heard footsteps coming from the corridor. Two scientists walked in, talking to each other. Mewtwo stared at them. He picked up his limp paws and hammered them against the glass with all his strength. Mewtwo winced.

_All of that, and all I manage to do is hurt my paws…_

One scientist looked at Mewtwo. He smirked at the pokemon.

"Save your energy, you worthless fool! Giovanni might need you later." The man in the lab coat smiled malevolently. He reached into his coat pocket and pulled out a purple-colored vial.

The Rocket strolled over to the control panel and inserted the vial into a slot in the machine. He pressed a button, and the vial started to empty. Moments later, purple smoke started billowing into the first three human's cells.

_What the-_

The smoke was so thick that nothing was visible for several minutes. When the smoke cleared, all three humans stood up. The woman started to utter incomprehensible grunts. She seemed to struggle against her voice.

"Gyrahh… ugh... whhaaay…"

Mewtwo's eyes widened.

"Whhyyyyaaaaaaahhhh!

The muscular man and the young child also started to babble, but slowly, their speech started to make sense.

"Why am I here? Where are we? Why am I different than before?"

The two Rocket scientists smiled with delight. "Soon, you three will join us and become part of Team Rocket!

_What? Is this what he's doing? Turing pokemon into humans to force them to join Team Rocket? Why bother?_

One Rocket scientist turned around and faced another machine with a screen on the front. He pressed a series of numbers into the control panel next to the screen. A picture of Giovanni popped up onto the screen.

"Sir, the human integration worked. They will be able to function in normal society in about two hours."

"Very well. Continue with the project as planned. Giovanni out."

The Rocket lifted his hand, turned off the monitor and turned toward Mewtwo.

"Sit tight… Mewtwo. You will soon know all you need to know."

Mewtwo glared at the scientist.

The Rocket simply smiled, and then left. The other scientist joined him.

_------------------------------------------_

Ho-oh stood in the clearing, surrounded by the other legendary pokemon as the meeting came to a close. It nodded at the others, then took off. The other legendaries followed, as they headed toward Johto, towards Silver Cave.

_------------------------------------------_

It had been two days since he tried to infiltrate the Rocket hideout with Mew. And failed. Mewtwo sat motionless in the transparent box, watching, waiting. He looked over toward Mew's box. She had woken up sometime in the night, and she looked forlornly at Mewtwo. Mewtwo watched as Mew sat up inside her cage.

_What the hell is going to happen now? How long are we going to stay here like this?_

The genetic pokemon turned toward the other "human's" cages. They paced their clear, glass-like cells. Last night, he had tried to communicate with them, and was successful. He now knew that the young boy with the violet hair had been a rattata, the muscular man with a bald head had been a rhyhorn, and the red-haired woman had been a rapidash. It had been difficult communicating though looks and gestures, but somehow he had managed it. Mewtwo turned his gaze toward the woman's cage. She looked up. Mewtwo continued to stare at the former rapidash. Her gaze quickly lowered and she turned away.

_Wait, I- never mind._

He quickly turned his eyes toward the entrance as the same two scientists entered once more.

"Good morning everyone, I trust you all slept well?" One scientist said with a deceitful smile.

The group tried to ignore the Rocket.

_What now?_

Walking toward the control panel, the scientist lifted his index finger and then pushed a button. Out of nowhere, binding ropes lashed out of the walls inside the human's enclosures and tied their arms. The doors to their clear cages swung open.

"You're coming with us."

_Oh no._

All the other humans slowly and unwillingly walked out of the cages, including Mew. Mewtwo sat up and placed his paws on the transparent wall.

_What about me? Are you just going to leave me here?_

The group slowly trailed their way out of the laboratory. Then, after a moment or two, Giovanni strolled inside the room.

"Hello Mewtwo."

The genetic pokemon sat down and stared malevolently at the Rocket leader.

"What do you want?"

"You."

"Why?"

"You will find out soon enough."

"Why? Tell me now Giovanni, or else!"

"Or else what? What do you think you can do?"

Mewtwo's face twisted into a scowl.

"Nothing."

"Correct, Mewtwo. Absolutely correct. But I will tell you one thing: You are about to become very useful to me."

"I'll never help you!"

"So you think."

Mewtwo's eyes narrowed.

"Tell me something Giovanni, why am I still in my pokemon form? Why have you turned Mew into a human? What purpose is there in doing that?"

"Very good, Mewtwo. Excellent question. I have no use for Mew, she does not fit into my specifications. You have so much more potential! I want you to do something for me. Something very important for the future of Team Rocket."

"I don't think so! Remember the first time you tried to do that, Giovanni? Your plans failed! I am more powerful than you can ever hope to handle! You think you can make me obey you, with a whip in one hand, and the other a closed fist? Think again. I won't help your organization, nor will I join it!"

"Most impressive Mewtwo. But, no matter how hard you try, your pathetic attempts to escape will be futile, and you will obey my every command. I see the power you hold inside. Power that I want, power that I need. You will make a fine commander for my new army!"


End file.
